@datagrok/helm 2.13.7 → 3.0.0

package/CREDITS.md

@@ -0,0 +1,164 @@
+# Helm — Third-Party Libraries
+
+The `@datagrok/helm` package is distributed under the MIT license that covers
+the rest of the `public/` repository (see [`../../LICENSE.md`](../../LICENSE.md)).
+It incorporates the open-source components listed below; this file reproduces
+the attribution and notices required by their respective licenses.
+
+All runtime dependencies bundled into the published artifact are under
+permissive licenses (MIT, ISC, BSD-3-Clause / Academic Free License v2.1).
+No copyleft (GPL/LGPL/MPL) component is bundled into the published Helm
+plugin artifact.
+
+The Pistoia HELM Web Editor and Scilligence JSDraw2 sources, which were
+historically vendored under `helm/JSDraw/`, are now consumed via
+`@datagrok-libraries/helm-web-editor` (an internal Datagrok library covered by
+the repo-wide MIT umbrella). Their original upstream licenses are reproduced
+below for completeness because the vendored copies remain in the repository.
+
+---
+
+## 1. Bundled in the published artifact (`dist/`)
+
+### Dojo Toolkit (1.10.10)
+
+The full Dojo Toolkit (`dojo`, `dijit`, `dojox`) is vendored under
+`vendor/dojo-1.10.10/` and webpack-bundled into a separate `package-dojo.js`
+chunk via `require.context()`. Required by JSDraw2 / HELM Web Editor.
+
+- Upstream: https://dojotoolkit.org/ — https://github.com/dojo/dojo
+- License: **BSD-3-Clause** OR **Academic Free License v2.1** (dual-licensed,
+  at the user's choice — Datagrok elects the BSD-3-Clause terms)
+
+```
+Dojo is available under *either* the terms of the BSD 3-Clause "New" License
+*or* the Academic Free License version 2.1. As a recipient of Dojo, you may
+choose which license to receive this code under.
+
+Copyright (c) 2005-2015, The Dojo Foundation
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+  * Redistributions of source code must retain the above copyright notice,
+    this list of conditions and the following disclaimer.
+  * Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
+  * Neither the name of the Dojo Foundation nor the names of its contributors
+    may be used to endorse or promote products derived from this software
+    without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+```
+
+**Modification note.** `core/client/d4`-style monkey patches are applied to
+Dojo at runtime (not in the vendored source) — see
+`HelmPackage.initHELMWebEditor()` in `src/package-utils.ts`, which patches
+`dojox.gfx.svg.Text.prototype.getTextWidth` to prevent an infinite loop. The
+vendored Dojo files themselves are byte-identical to the upstream 1.10.10
+release.
+
+### Scilligence JSDraw2 Lite & Pistoia HELM Web Editor (vendored copy under `helm/JSDraw/`)
+
+Historically vendored uncompressed sources of the JSDraw2 Lite molecule
+sketcher (Scilligence) and the Pistoia HELM Web Editor. The active code path
+loads `@datagrok-libraries/helm-web-editor` (the internal Datagrok library)
+rather than these files; they are kept in the repository as a reference and
+fallback. If a build configuration ever bundles them again, the following
+notice applies.
+
+- Upstream (JSDraw2 Lite): https://github.com/scilligence/JSDraw.Lite
+- Upstream (HELM Web Editor): https://github.com/PistoiaHELM/HELMWebEditor
+- License: **MIT** (both projects)
+
+```
+The MIT License (MIT)
+
+Copyright (c) Scilligence Corporation (JSDraw2 Lite) and the Pistoia Alliance
+(HELM Web Editor)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+### lru-cache (10.4.x)
+
+LRU cache used to cap the rendered-monomer / off-screen-editor caches in the
+HELM cell renderer.
+
+- Upstream: https://github.com/isaacs/node-lru-cache
+- License: **ISC**
+
+```
+The ISC License
+
+Copyright (c) 2010-2023 Isaac Z. Schlueter and Contributors
+
+Permission to use, copy, modify, and/or distribute this software for any
+purpose with or without fee is hereby granted, provided that the above
+copyright notice and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR
+IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+```
+
+---
+
+## 2. Linked at runtime via the Datagrok platform (webpack externals)
+
+These libraries are not bundled into Helm's `dist/` — they are provided once
+by the platform host and shared across all packages.
+
+| Component       | Version | License      | Upstream                                   |
+|-----------------|---------|--------------|--------------------------------------------|
+| OpenChemLib JS  | 7.x     | BSD-3-Clause | https://github.com/cheminfo/openchemlib-js |
+| RxJS            | 6.x     | Apache-2.0   | https://github.com/ReactiveX/rxjs          |
+| cash-dom        | 8.x     | MIT          | https://github.com/fabiospampinato/cash    |
+| Day.js          | 1.x     | MIT          | https://github.com/iamkun/dayjs            |
+| wu.js           | 2.x     | MIT          | https://github.com/fitzgen/wu.js           |
+
+---
+
+## 3. Development-only dependencies
+
+Tools used during the build/test cycle (not in the runtime tree, not bundled):
+the `datagrok-tools` CLI transitively pulls in `puppeteer-screen-recorder`,
+which references `@ffmpeg-installer/ffmpeg` (LGPL-2.1) and
+`@ffmpeg-installer/win32-x64` (GPLv3). These binaries are **not** redistributed
+as part of the published Helm plugin and impose no obligation on users of the
+plugin.
+
+The peer/devDependencies on other Datagrok plugins (`@datagrok/bio`,
+`@datagrok/chem`) are MIT — covered by the repo-wide `LICENSE.md`. Each of
+those plugins maintains its own `CREDITS.md` for its own third-party content.

package/dist/489.js

@@ -0,0 +1,2 @@
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e=this.getSelection();""===e.preview||null===this._favHooks||this._favHooks.toggleFavoriteTriplet(e.sugar,e.base,e.linker)};t.addEventListener("click",e),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&e(t)}),this._favStar=t,r.appendChild(t)}this.element.appendChild(r),this._hintEl=ot(this._doc,"div",{class:"hw-rna-builder__hint","data-testid":"rna-builder-hint",hidden:!0}),this.element.appendChild(this._hintEl);let l=this._buildSvg();this.element.appendChild(l),this._preview=ot(this._doc,"div",{class:"hw-rna-builder__preview","data-testid":"rna-builder-preview"}),this.element.appendChild(this._preview),this._addBtn=ot(this._doc,"button",{class:"hw-rna-builder__add",type:"button","data-testid":"rna-builder-add-btn"},["Add triplet"]),this._addBtn.addEventListener("click",()=>this._onAddClicked()),this.element.appendChild(this._addBtn),t.appendChild(this.element);let s=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),o=e.on("theme:change",()=>{this._destroyed||this._repaintSlotColors()});this._libUnsub=()=>{try{s()}catch{}try{o()}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}getSelection(){let t=this._slots.get("sugar")?.value??"",e=this._slots.get("base")?.value??"",i=this._slots.get("linker")?.value??"";return{sugar:t,base:e,linker:i,preview:""!==t&&""!==e&&""!==i?mt(t,e,i):""}}setField(t,e){let i=this._slots.get(t);void 0!==i&&(i.value=e,this._setLabelText(i.labelEl,e),this._repaintSlot(i),this._updatePreview(),this.onValueSet.next({field:t,symbol:e}))}startPickMode(t){this._pickMode!==t?(null!==this._pickMode&&this._setSlotPressed(this._pickMode,!1),this._pickMode=t,this._setSlotPressed(t,!0),this._setHintActive(t),this.onPickModeChange.next({field:t}),null!==this._hooks&&this._hooks.beginBiotypeFilter(vt[t],e=>{this.setField(t,e),this._exitPickMode()},()=>{this._exitPickMode()})):this.cancelPickMode()}cancelPickMode(){null!==this._pickMode&&(null!==this._hooks&&this._hooks.endBiotypeFilter(),this._exitPickMode())}getPickMode(){return this._pickMode}triggerAdd(){this._onAddClicked()}destroy(){this._destroyed||(this._destroyed=!0,null!==this._pickMode&&null!==this._hooks&&this._hooks.endBiotypeFilter(),this._libUnsub(),this.onValueSet.complete(),this.onPickModeChange.complete(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}_buildSvg(){let t=this._doc.createElementNS(gt,"svg");t.setAttribute("class","hw-rna-builder__triplet"),t.setAttribute("viewBox","0 0 200 180"),t.setAttribute("data-testid","rna-builder-triplet-svg"),t.setAttribute("role","group"),t.setAttribute("aria-label","Triplet preview");let e=this._doc.createElementNS(gt,"line");e.setAttribute("class","hw-rna-builder__bond"),e.setAttribute("x1",String(wt.x+18)),e.setAttribute("y1",String(wt.y)),e.setAttribute("x2",String(At.x-18)),e.setAttribute("y2",String(At.y)),t.appendChild(e);let i=this._doc.createElementNS(gt,"line");i.setAttribute("class","hw-rna-builder__bond"),i.setAttribute("x1",String(wt.x)),i.setAttribute("y1",String(wt.y+18)),i.setAttribute("x2",String(St.x)),i.setAttribute("y2",String(St.y-22)),t.appendChild(i);let r=this._doc.createElementNS(gt,"rect");r.setAttribute("class","hw-rna-builder__slot-shape"),r.setAttribute("x",String(-18)),r.setAttribute("y",String(-18)),r.setAttribute("width",String(36)),r.setAttribute("height",String(36)),r.setAttribute("rx","8"),r.setAttribute("ry","8");let l=this._buildSlot("sugar","Pick sugar (backbone)",wt,r),s=this._doc.createElementNS(gt,"circle");s.setAttribute("class","hw-rna-builder__slot-shape"),s.setAttribute("cx","0"),s.setAttribute("cy","0"),s.setAttribute("r",String(18));let o=this._buildSlot("linker","Pick linker",At,s),n=this._doc.createElementNS(gt,"path");n.setAttribute("class","hw-rna-builder__slot-shape"),n.setAttribute("d","M -22 0 L 0 -22 L 22 0 L 0 22 Z");let a=this._buildSlot("base","Pick base",St,n);return t.appendChild(o.groupEl),t.appendChild(l.groupEl),t.appendChild(a.groupEl),this._slots.set("sugar",l),this._slots.set("linker",o),this._slots.set("base",a),t}_buildSlot(t,e,i,r){let l=this._doc.createElementNS(gt,"g");l.setAttribute("class","hw-rna-builder__slot"),l.setAttribute("data-slot",t),l.setAttribute("data-testid",`rna-builder-slot-${t}`),l.setAttribute("role","button"),l.setAttribute("tabindex","0"),l.setAttribute("aria-label",e),l.setAttribute("aria-pressed","false"),l.setAttribute("transform",`translate(${i.x} ${i.y})`),l.appendChild(r);let s=this._doc.createElementNS(gt,"text");s.setAttribute("class","hw-rna-builder__slot-label"),s.setAttribute("data-testid",`rna-builder-${t}-value`),s.setAttribute("x","0"),s.setAttribute("y","0"),s.setAttribute("text-anchor","middle"),s.setAttribute("dominant-baseline","central"),l.appendChild(s);let o=e=>{e.stopPropagation(),this.startPickMode(t)};return l.addEventListener("click",o),l.addEventListener("keydown",t=>{let e=t;("Enter"===e.key||" "===e.key)&&o(t)}),l.addEventListener("mouseenter",e=>this._showSlotTooltip(t,e)),l.addEventListener("mouseleave",()=>this._hideSlotTooltip()),l.addEventListener("focus",()=>this._showSlotTooltip(t,null)),l.addEventListener("blur",()=>this._hideSlotTooltip()),{id:t,biotype:vt[t],groupEl:l,shapeEl:r,labelEl:s,value:""}}_setLabelText(t,e){let i=[];for(let e=t.firstChild;null!==e;e=e.nextSibling)"title"===e.nodeName||"TITLE"===e.nodeName||i.push(e);for(let e of i)t.removeChild(e);let r=function(t){let e=t.length;return e<=2?16:e<=4?11:e<=7?8:e<=10?6:5}(e);t.setAttribute("font-size",String(r)),t.setAttribute("text-anchor","middle"),t.setAttribute("dominant-baseline","central");let l=e.length>10?`${e.slice(0,9)}…`:e;t.appendChild(this._doc.createTextNode(l));let s=t.parentNode;if(null!==s){let t=null;for(let e=s.firstChild;null!==e;e=e.nextSibling)if("title"===e.nodeName||"TITLE"===e.nodeName){t=e;break}for(null===t&&(t=this._doc.createElementNS(gt,"title"),s.insertBefore(t,s.firstChild));null!==t.firstChild;)t.removeChild(t.firstChild);t.appendChild(this._doc.createTextNode(e))}}_repaintSlotColors(){for(let t of this._slots.values())this._repaintSlot(t)}_repaintSlot(t){let e=this._editor.getService().monomerLib,i=this._theme(),r=""===t.value?null:function(t,e,i){return t.getMonomerSet(e).get(i)??null}(e,t.biotype,t.value),l=$(r,t.biotype,i.colorTheme);t.shapeEl.style.fill=l.background,t.shapeEl.style.stroke=l.line,t.labelEl.style.fill=l.text}_populateDefaults(){let t=this._editor.getService().monomerLib;for(let[e,i]of this._slots.entries()){let r=Tt(t,i.biotype),l=Et(r,yt[e]),s=""!==i.value&&r.some(t=>t.symbol===i.value)?i.value:l??r[0]?.symbol??"";i.value=s,this._setLabelText(i.labelEl,s)}}_updatePreview(){let t=this.getSelection();for(;null!==this._preview.firstChild;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(""===t.preview?"-":t.preview)),this._updateFavStar(t)}_updateFavStar(t){if(null===this._favStar||null===this._favHooks)return;let e=""!==t.preview,i=e&&this._favHooks.isFavoriteTriplet(t.sugar,t.base,t.linker);for(;null!==this._favStar.firstChild;)this._favStar.removeChild(this._favStar.firstChild);this._favStar.appendChild(this._doc.createTextNode(i?"★":"☆")),this._favStar.setAttribute("aria-pressed",i?"true":"false"),e?this._favStar.removeAttribute("aria-disabled"):this._favStar.setAttribute("aria-disabled","true");let r="hw-rna-builder__fav"+(i?" hw-rna-builder__fav--active":"")+(e?"":" hw-rna-builder__fav--disabled");this._favStar.setAttribute("class",r)}_onAddClicked(){let t=this.getSelection();""!==t.preview&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)}_exitPickMode(){if(null===this._pickMode)return;let t=this._pickMode;this._setSlotPressed(t,!1),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null})}_setHintActive(t){let e=this._hintEl;for(;null!==e.firstChild;)e.removeChild(e.firstChild);if(null===t)return void e.setAttribute("hidden","");e.removeAttribute("hidden");let i="sugar"===t?"sugar":"base"===t?"base":"linker";e.appendChild(this._doc.createTextNode(`Pick ${i} from palette`))}_setSlotPressed(t,e){let i=this._slots.get(t);if(void 0===i)return;i.groupEl.setAttribute("aria-pressed",e?"true":"false");let r=(i.groupEl.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-rna-builder__slot--active"!==t).join(" ");i.groupEl.setAttribute("class",e?`${r} hw-rna-builder__slot--active`:r)}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_builderRdkitSvgFor(e){if(null===e)return null;let i=e.smiles;if(void 0===i||""===i)return null;let r=this._rdkit();if(null===r)return null;let l=`${e.polymerType}:${e.symbol}`;if(this._builderRdkitCache.has(l))return this._builderRdkitCache.get(l)??null;let s=nt(r,i,220,140);if(this._builderRdkitCache.size>=t._BUILDER_RDKIT_CACHE_LIMIT){let t=this._builderRdkitCache.keys().next().value;void 0!==t&&this._builderRdkitCache.delete(t)}return this._builderRdkitCache.set(l,s),s}_slotHint(t){switch(t){case"sugar":return"Click to choose a different sugar";case"base":return"Click to choose a different base";case"linker":return"Click to choose a different linker"}}_slotTitle(t,e){let i=""===e?"?":e;switch(t){case"sugar":return`Sugar: ${i}`;case"base":return`Base: ${i}`;case"linker":return`Linker: ${i}`}}_showSlotTooltip(t,e){let i=this._slots.get(t);if(void 0===i)return;let r=this._editor.getService().monomerLib.getMonomerSet(i.biotype),l=""===i.value?null:r.get(i.value)??null,s=at(this._doc,"builder-tooltip","hw-builder-tooltip");ht(this._doc,s,{symbol:this._slotTitle(t,i.value),name:l?.name??"",rdkitSvg:this._builderRdkitSvgFor(l),rdkitTestid:"builder-tooltip-rdkit-svg",hint:this._slotHint(t)});let o=e;if(null!==o&&"number"==typeof o.clientX&&"number"==typeof o.clientY)dt(s,o.clientX,o.clientY);else{let t=i.groupEl,e="function"==typeof t.getBoundingClientRect?t.getBoundingClientRect():null;null!==e?dt(s,e.left+e.width/2,e.top+e.height/2):dt(s,0,0)}}_hideSlotTooltip(){ut(this._doc.body.querySelector('[data-testid="builder-tooltip"]'))}};kt._BUILDER_RDKIT_CACHE_LIMIT=256;var Ct=kt;function Tt(t,e){let i=t.getMonomerSet(e),r=[];for(let t of i.values())r.push(t);return r.sort((t,e)=>t.symbol.localeCompare(e.symbol)),r}function Et(t,e){let i=new Set;for(let e of t)i.add(e.symbol);for(let t of e)if(i.has(t))return t;return null}var Nt="Favorites",Mt={[Nt]:"★ Favorites",[d.PEPTIDE]:"Peptides",[d.RNA]:"RNA",[d.CHEM]:"CHEM",[d.BLOB]:"BLOB",G:"G"},xt=[Nt,d.PEPTIDE,d.RNA,d.CHEM,d.BLOB,"G"],Bt="hwe:palette:favorites",Lt="hwe:palette:active-tab";function It(t){return`${t.sugar}|${t.base}|${t.linker}`}var Pt=class t{constructor(t,e,i){this.favoritesChanged=new u,this._nextAddUnsub=()=>{},this._favorites=new Set,this._favoriteTriplets=[],this._pendingRnaSelection=null,this._visibleTabs=[Nt],this._activeTab=Nt,this._searchInput=null,this._filter="",this._destroyed=!1,this._rnaBuilder=null,this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,this._pickEscapeListener=null,this._pickOutsideClickListener=null,this._paletteRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??st(t),this._opts={documentImpl:this._doc,groupByNaturalAnalog:i?.groupByNaturalAnalog??!0,allowFavorites:i?.allowFavorites??!0},this._loadFavorites(),this._activeTab=this._resolveInitialTab(i?.initialTab),this.element=ot(this._doc,"div",{class:"hw-palette","data-testid":"palette"}),t.appendChild(this.element),this._render(),this._libUnsub=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),this._themeUnsub=e.on("theme:change",()=>{this._destroyed||this.refresh()}),this._nextAddUnsub=e.on("option:change",t=>{this._destroyed||"nextAdd"===t.key&&this._updatePrimedClasses()})}refresh(){this._render()}setFilter(t){this._filter=t.trim().toLowerCase(),null!==this._searchInput&&this._searchInput.value!==t&&(this._searchInput.value=t),this._applyFilter()}setActiveTab(t){this._visibleTabs.includes(t)&&(this._activeTab=t,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter())}getActiveTab(){return this._activeTab}getFavorites(){let t=this._editor.getService().monomerLib,e=[];for(let i of this._favorites)null!==this._findMonomer(t,i)&&e.push(i);return e}setFavorite(t,e){e!==this._favorites.has(t)&&(e?this._favorites.add(t):this._favorites.delete(t),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}clearFavorites(){0===this._favorites.size&&0===this._favoriteTriplets.length||(this._favorites.clear(),this._favoriteTriplets.length=0,this._saveFavorites(),this._render(),this._emitFavoritesChanged())}getFavoriteTriplets(){return this._favoriteTriplets.map(t=>({...t}))}isFavoriteTriplet(t,e,i){let r=It({sugar:t,base:e,linker:i});return this._favoriteTriplets.some(t=>It(t)===r)}setFavoriteTriplet(t,e,i,r){let l=It({sugar:t,base:e,linker:i}),s=this._favoriteTriplets.findIndex(t=>It(t)===l);r!==s>=0&&(r?this._favoriteTriplets.push({sugar:t,base:e,linker:i}):this._favoriteTriplets.splice(s,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}_hidePaletteTooltips(){let t=this._doc.body;ut(t.querySelector('[data-testid="palette-tooltip"]')),ut(t.querySelector('[data-testid="palette-triplet-tooltip"]'))}_emitFavoritesChanged(){this.favoritesChanged.next({favorites:this.getFavorites(),triplets:this.getFavoriteTriplets()})}destroy(){this._destroyed||(this._destroyed=!0,null!==this._rnaBuilder&&(this._rnaBuilder.destroy(),this._rnaBuilder=null),this._libUnsub(),this._themeUnsub(),this._nextAddUnsub(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}getRnaBuilder(){return this._rnaBuilder}hasActiveBiotypeFilter(){return null!==this._activeBiotypeFilter}getActiveBiotypeFilter(){return this._activeBiotypeFilter}cancelBiotypeFilter(){if(null===this._activeBiotypeFilter)return;let t=this._pickCanceller;this._teardownPickMode(),t?.()}_buildPaletteFilterHooks(){return{beginBiotypeFilter:(t,e,i)=>{null!==this._activeBiotypeFilter&&this._teardownPickMode(),this._activeBiotypeFilter=t,this._pickResolver=e,this._pickCanceller=i,this._applyFilter();let r=t=>{"Escape"===t.key&&this.cancelBiotypeFilter()};this._pickEscapeListener=r,this._doc.defaultView?.addEventListener("keydown",r);let l=t=>{if(null===this._activeBiotypeFilter)return;let e=t.target;if(null==e)return;let i=this._activeBiotypeFilter,r=e;for(;null!==r;){let t=void 0===r.getAttribute?null:r.getAttribute("class");if(null!==t){let e=t.split(/\s+/);if(e.includes("hw-palette__tile")){if((r.getAttribute("data-biotype")??"")===i)return;break}if(e.includes("hw-rna-builder__slot")){if(this._isInsideOwnPalette(r))return;break}}r=r.parentElement}this.cancelBiotypeFilter()};this._pickOutsideClickListener=l,this._doc.addEventListener("mousedown",l,!0)},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let t=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`);if(null===t)return;let e=t;try{if("function"==typeof e.scrollTo)return void e.scrollTo({top:0,behavior:"smooth"})}catch{}"number"==typeof e.scrollTop&&(e.scrollTop=0)}_isInsideOwnPalette(t){let e=t;for(;null!==e;){if(e===this.element)return!0;e=e.parentElement}return!1}_teardownPickMode(){null!==this._activeBiotypeFilter&&(this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,null!==this._pickEscapeListener&&(this._doc.defaultView?.removeEventListener("keydown",this._pickEscapeListener),this._pickEscapeListener=null),null!==this._pickOutsideClickListener&&(this._doc.removeEventListener("mousedown",this._pickOutsideClickListener,!0),this._pickOutsideClickListener=null),this._applyFilter())}_render(){for(null!==this._rnaBuilder&&(this._pendingRnaSelection=this._rnaBuilder.getSelection(),this._rnaBuilder.destroy(),this._rnaBuilder=null);null!==this.element.firstChild;)this.element.removeChild(this.element.firstChild);let t=this._doc.createElement("input");t.setAttribute("type","search"),t.setAttribute("class","hw-palette__search"),t.setAttribute("placeholder","Search monomers..."),t.setAttribute("data-testid","palette-search"),""!==this._filter&&(t.value=this._filter),t.addEventListener("input",()=>this.setFilter(t.value)),this._searchInput=t,this.element.appendChild(t),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=Nt);let e=ot(this._doc,"div",{class:"hw-palette__tabs",role:"tablist","data-testid":"palette-tabs"});for(let t of this._visibleTabs){let i=t===this._activeTab,r=ot(this._doc,"button",{class:"hw-palette__tab",type:"button",role:"tab","aria-controls":`hw-palette-pane-${t}`,"aria-selected":i?"true":"false","data-testid":`palette-tab-${t}`,"data-tab":t,title:Mt[t]},[Mt[t]]);r.addEventListener("click",()=>this.setActiveTab(t)),e.appendChild(r)}this.element.appendChild(e);let i=ot(this._doc,"div",{class:"hw-palette__panes"}),r=this._theme(),l=this._editor.getService().monomerLib;for(let t of this._visibleTabs){let e=t===this._activeTab,s=ot(this._doc,"div",{class:"hw-palette__pane",id:`hw-palette-pane-${t}`,role:"tabpanel","data-testid":`palette-pane-${t}`,"data-tab":t,hidden:!e});t===Nt?this._buildFavoritesPane(s,l,r):this._buildPolymerPane(s,t,l,r),i.appendChild(s)}this.element.appendChild(i),this._applyFilter()}_computeVisibleTabs(){let t=this._editor.getService().monomerLib,e=new Set;for(let i of t.getPolymerTypes())e.add(i);let i=[];i.push(Nt);for(let t of xt)t!==Nt&&e.has(t)&&i.push(t);return i}_buildFavoritesPane(t,e,i){let r=this._resolveFavoriteMonomers(e),l=this._favoriteTriplets;if(0===r.length&&0===l.length){let e=ot(this._doc,"div",{class:"hw-palette__placeholder","data-testid":"palette-favorites-empty"},["No favorites yet — click the ☆ on any tile to add one."]);return void t.appendChild(e)}for(let[e,i]of this._groupByPolymerAndType(r))t.appendChild(this._renderGroup(e,i));l.length>0&&t.appendChild(this._renderTripletGroup("RNA · Triplets",l,e))}_groupByPolymerAndType(t){let e=new Map;for(let i of t){let t=i.polymerType,r=i.monomerType??"Undefined",l=`${t}|${r}`,s=e.get(l);void 0===s&&(s={pt:t,mt:r,list:[]},e.set(l,s)),s.list.push(i)}let i=t=>{let e=xt.indexOf(t);return e<0?99:e},r={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(e.values()).sort((t,e)=>i(t.pt)-i(e.pt)||(r[t.mt]??9)-(r[e.mt]??9)||t.mt.localeCompare(e.mt)).map(t=>[`${this._polymerLabel(t.pt)} · ${t.mt}`,t.list])}_polymerLabel(t){return Mt[t]??t}_renderTripletGroup(t,e,i){let r=ot(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),l=ot(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),s=ot(this._doc,"div",{class:"hw-triplet-chips","data-testid":"palette-triplet-favorites"});for(let t of e)s.appendChild(this._renderTripletChip(t,i));return r.appendChild(l),r.appendChild(s),r}_renderTripletChip(t,e){let i=mt(t.sugar,t.base,t.linker),r=e.getMonomerSet(s).get(t.base)??null,l=$(r,s,this._theme().colorTheme),o=this.isFavoriteTriplet(t.sugar,t.base,t.linker),n=void 0!==r?.name&&""!==r.name?`${i} — ${r.name}`:i,{root:a}=function(t,e){let i=!1!==e.showStar,r=ot(t,"span",{class:"hw-triplet-chip__star"},[e.favorite?"★":"☆"]),l=ot(t,"span",{class:"hw-triplet-chip__label"},[e.label]),s=["hw-triplet-chip"];e.favorite&&s.push("hw-triplet-chip--favorite");let o=i?[r,l]:[l];return{root:ot(t,"div",{class:s.join(" "),role:"button",tabindex:"0","aria-label":e.title,"data-sugar":e.sugar,"data-base":e.base,"data-linker":e.linker,"data-triplet":e.label,"data-testid":`palette-triplet-${e.label}`,title:e.title,style:`background:${e.background};color:${e.textColor};`},o),star:r}}(this._doc,{sugar:t.sugar,base:t.base,linker:t.linker,label:i,title:n,background:y(l.background),textColor:l.text,favorite:o,showStar:this._opts.allowFavorites});return this._wireTripletChip(a,t),a}_wireTripletChip(t,e){t.addEventListener("mouseenter",t=>{let i=t,r=at(this._doc,"palette-triplet-tooltip","hw-palette-tooltip hw-triplet-tooltip");(function(t,e,i){for(;null!==e.firstChild;)e.removeChild(e.firstChild);e.appendChild(ot(t,"div",{class:"hw-tooltip__symbol"},[i.title]));let r=ot(t,"div",{class:"hw-tooltip__triplet"});for(let e of i.parts){let l=ot(t,"div",{class:"hw-tooltip__triplet-part"});if(l.appendChild(ot(t,"div",{class:"hw-tooltip__triplet-role"},[`${e.role}: ${e.symbol}`])),void 0!==e.name&&""!==e.name&&e.name!==e.symbol&&l.appendChild(ot(t,"div",{class:"hw-tooltip__name"},[e.name])),void 0!==e.rdkitSvg&&null!==e.rdkitSvg&&""!==e.rdkitSvg){let r={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(r["data-testid"]=i.rdkitTestid);let s=ot(t,"div",r);s.innerHTML=e.rdkitSvg,l.appendChild(s)}r.appendChild(l)}e.appendChild(r),void 0!==i.hint&&""!==i.hint&&e.appendChild(ot(t,"div",{class:"hw-tooltip__hint"},[i.hint]))})(this._doc,r,{title:mt(e.sugar,e.base,e.linker),parts:this._tripletTooltipParts(e),hint:"Click to add this triplet",rdkitTestid:"palette-triplet-tooltip-rdkit-svg"}),dt(r,"number"==typeof i.clientX?i.clientX:0,"number"==typeof i.clientY?i.clientY:0)}),t.addEventListener("mouseleave",()=>{ut(this._doc.body.querySelector('[data-testid="palette-triplet-tooltip"]'))}),t.addEventListener("click",t=>{let i=t.target;if(this._opts.allowFavorites&&!0===i?.classList?.contains("hw-triplet-chip__star"))return this.setFavoriteTriplet(e.sugar,e.base,e.linker,!this.isFavoriteTriplet(e.sugar,e.base,e.linker)),void t.stopPropagation();this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)}),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)})}_buildRnaDefaultChips(e){let i=this._pickSymbol(e.getMonomerSet(l),["r","R"]),r=this._pickSymbol(e.getMonomerSet(o),["p","P"]),n=e.getMonomerSet(s);if(null===i||null===r)return null;let a=t._DEFAULT_TRIPLET_BASES.filter(t=>n.has(t));if(0===a.length)return null;let h=ot(this._doc,"div",{class:"hw-triplet-chips hw-triplet-chips--defaults","data-testid":"rna-default-triplets"});for(let t of a)h.appendChild(this._renderTripletChip({sugar:i,base:t,linker:r},e));return h}_tripletTooltipParts(t){let e=this._editor.getService().monomerLib,i=(t,i,r)=>{let l=e.getMonomerSet(i).get(r)??null;return{role:t,symbol:r,...void 0!==l?.name?{name:l.name}:{},rdkitSvg:null===l?null:this._paletteRdkitSvg(l)}};return[i("Sugar",l,t.sugar),i("Base",s,t.base),i("Linker",o,t.linker)]}_pickSymbol(t,e){for(let i of e)if(t.has(i))return i;let i=t.keys().next();return!0===i.done?null:i.value}_restoreRnaSelection(){let t=this._pendingRnaSelection;if(this._pendingRnaSelection=null,null===t||null===this._rnaBuilder)return;let e=this._editor.getService().monomerLib;""!==t.sugar&&e.getMonomerSet(l).has(t.sugar)&&this._rnaBuilder.setField("sugar",t.sugar),""!==t.base&&e.getMonomerSet(s).has(t.base)&&this._rnaBuilder.setField("base",t.base),""!==t.linker&&e.getMonomerSet(o).has(t.linker)&&this._rnaBuilder.setField("linker",t.linker)}_resolveFavoriteMonomers(t){let e=[];for(let i of this._favorites){let r=this._findMonomer(t,i);null!==r&&e.push(r)}return e}_findMonomer(t,e){for(let i of t.getPolymerTypes()){let r=t.getMonomer(i,e);if(null!==r)return r}return null}_buildPolymerPane(t,e,i,r){let l=e,s=this._monomersForPolymer(l,i);if(0===s.length)return;if(l===d.RNA){this._rnaBuilder=new Ct(t,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(t,e,i)=>this.isFavoriteTriplet(t,e,i),toggleFavoriteTriplet:(t,e,i)=>this.setFavoriteTriplet(t,e,i,!this.isFavoriteTriplet(t,e,i))}:null}),this._restoreRnaSelection();let e=this._buildRnaDefaultChips(i);null!==e&&t.appendChild(e);let r=this._groupRna(s);for(let[e,i]of r)0!==i.length&&t.appendChild(this._renderGroup(e,i));return}if(l===d.PEPTIDE&&this._opts.groupByNaturalAnalog){let e=this._groupByAnalog(s);for(let[i,r]of e){let e=""===i?"Other":i;t.appendChild(this._renderGroup(e,r))}return}let o=ot(this._doc,"div",{class:"hw-palette__group-tiles"}),n=this._editor.getNextAddSymbol(),a=this._sortByColor(s);for(let t of a){let e=this._biotype(t,l);o.appendChild(this._renderTile(t,e,n))}t.appendChild(o)}_renderGroup(t,e){let i=ot(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),r=ot(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),l=ot(this._doc,"div",{class:"hw-palette__group-tiles"}),s=this._editor.getNextAddSymbol(),o=this._sortByColor(e);for(let t of o){let e=this._biotype(t,t.polymerType);l.appendChild(this._renderTile(t,e,s))}return i.appendChild(r),i.appendChild(l),i}_sortByColor(t){let e=this._theme(),i=t.map((t,i)=>{let r=function(t){let e=_(t);if(null===e)return{h:0,s:0,l:0};let[i,r,l]=m(e[0],e[1],e[2]);return{h:i,s:r,l}}($(t,this._biotype(t,t.polymerType),e.colorTheme).background),l=0===r.s?1:0;return{m:t,idx:i,h:r.h,s:r.s,l:r.l,isGrey:l}});return i.sort((t,e)=>t.isGrey!==e.isGrey?t.isGrey-e.isGrey:t.h!==e.h?t.h-e.h:t.s!==e.s?t.s-e.s:t.l!==e.l?t.l-e.l:t.idx-e.idx),i.map(t=>t.m)}_monomersForPolymer(t,e){let i=e.getMonomerSymbolsByType(t),r=[];for(let l of i){let i=e.getMonomer(t,l);null!==i&&r.push(i)}return r.sort((t,e)=>t.symbol.localeCompare(e.symbol)),r}_groupByAnalog(t){let e=new Map;for(let i of t){let t=i.naturalAnalog??"",r=e.get(t);void 0===r&&(r=[],e.set(t,r)),r.push(i)}let i=[],r=Array.from(e.keys()).sort((t,e)=>""===t&&""!==e?1:""===e&&""!==t?-1:t.localeCompare(e));for(let t of r)i.push([t,e.get(t)]);return new Map(i)}_groupRna(t){let e=[],i=[],r=[],n=[];for(let a of t){let t=F(a);t===l?e.push(a):t===s?i.push(a):t===o?r.push(a):n.push(a)}let a=new Map;return a.set("Backbones",e),a.set("Bases",i),a.set("Linkers",r),n.length>0&&a.set("Other",n),a}_renderTile(t,e,i){let r=this._favorites.has(t.symbol),l=null!==i&&i.symbol===t.symbol&&i.biotype===e,{root:s,star:o}=function(t,e){let i=$(e.monomer,e.biotype,e.theme.colorTheme),r=y(i.background),l=i.text,s=function(t,e){let i=w(t),r=w(e);return(Math.max(i,r)+.05)/(Math.min(i,r)+.05)}(l,r)<5,o=e.monomer.symbol,n=function(t){return t<=3?14:t<=6?11:t<=9?9:8}(o.length),a=`font-size:${n}px;${o.length>=10?"line-height:1.1;letter-spacing:-0.02em;":""}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:80px;display:inline-block;`,h=ot(t,"span",{class:"hw-palette__star"},[e.favorite?"★":"☆"]),d=ot(t,"span",{class:"hw-palette__label",style:a},[o]),u=["hw-palette__tile"];e.primed&&u.push("hw-palette__tile--primed"),e.favorite&&u.push("hw-palette__tile--favorite"),s&&u.push("hw-palette__tile--low-contrast");let c=void 0!==e.monomer.name?`${o} — ${e.monomer.name}`:o,p=`background:${r};color:${l};width:100%;min-width:48px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return{root:ot(t,"div",{class:u.join(" "),draggable:"true",role:"button","aria-pressed":e.primed?"true":"false","aria-label":c,"data-symbol":o,"data-biotype":e.biotype,"data-bg":r,"data-raw-bg":i.background,"data-testid":`palette-tile-${o}`,title:c,style:p},[h,d]),star:h}}(this._doc,{monomer:t,biotype:e,theme:this._theme(),favorite:r,primed:l});return this._wireTile(s,o,t,e),s}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_paletteRdkitSvg(e){let i=e.smiles;if(void 0===i||""===i)return null;let r=this._rdkit();if(null===r)return null;let l=`${e.polymerType}:${e.symbol}`;if(this._paletteRdkitCache.has(l))return this._paletteRdkitCache.get(l)??null;let s=nt(r,i,220,140);if(this._paletteRdkitCache.size>=t._PALETTE_RDKIT_CACHE_LIMIT){let t=this._paletteRdkitCache.keys().next().value;void 0!==t&&this._paletteRdkitCache.delete(t)}return this._paletteRdkitCache.set(l,s),s}_wireTile(t,e,i,r){t.addEventListener("mouseenter",t=>{let e=t,r=at(this._doc,"palette-tooltip","hw-palette-tooltip");ht(this._doc,r,{symbol:i.symbol,name:i.name??"",rdkitSvg:this._paletteRdkitSvg(i),rdkitTestid:"palette-tooltip-rdkit-svg"}),dt(r,"number"==typeof e.clientX?e.clientX:0,"number"==typeof e.clientY?e.clientY:0)}),t.addEventListener("mouseleave",()=>{ut(this._doc.body.querySelector('[data-testid="palette-tooltip"]'))}),t.addEventListener("click",t=>{let e=t.target;if(this._opts.allowFavorites&&void 0!==e&&!0===e?.classList?.contains("hw-palette__star"))return this.setFavorite(i.symbol,!this._favorites.has(i.symbol)),void t.stopPropagation();if(null!==this._activeBiotypeFilter&&this._activeBiotypeFilter===r){let e=this._pickResolver;return this._teardownPickMode(),e?.(i.symbol),this._scrollActivePaneToTop(),void t.stopPropagation()}let l=this._editor.getSelection();if(l.atoms.size>0){let e=this._editor.getMol(),s=[];for(let t of l.atoms){let i=e.atoms.find(e=>e.id===t);void 0!==i&&s.push(i)}return s.length>0&&s.every(t=>t.biotype===r)?(this._editor.replaceMonomers(s,i.symbol),void t.stopPropagation()):(this._editor.fire("editor:status",{message:`Cannot bulk-replace ${s.length} selected atom(s) with ${i.symbol}: selection contains incompatible biotypes for ${r}.`,severity:"warn",durationMs:3e3}),void t.stopPropagation())}let s=this._editor.getNextAddSymbol();if(null!==s&&s.symbol===i.symbol&&s.biotype===r)return this._editor.setNextAddSymbol(null),void this._updatePrimedClasses();this._editor.setNextAddSymbol(i.symbol,r),this._updatePrimedClasses()}),t.addEventListener("dragstart",t=>{let e=t.dataTransfer;if(null!=e)try{e.setData("application/x-hwe-monomer",JSON.stringify({symbol:i.symbol,biotype:r})),e.effectAllowed="copy"}catch{}ut(this._doc.body.querySelector('[data-testid="palette-tooltip"]')),this._editor.startPaletteDrag(i.symbol,r)})}_biotype(t,e){let i=F(t);if(null!==i)return i;switch(e){case d.PEPTIDE:return r;case d.RNA:return l;case d.CHEM:return n;case d.BLOB:return a;default:return n}}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_applyFilter(){let t=this._filter,e=this._activeBiotypeFilter,i=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`),r=(i??this.element).querySelectorAll(".hw-palette__tile");for(let i=0;i<r.length;i++){let l=r[i],s=(l.getAttribute("data-symbol")??"").toLowerCase(),o=(l.getAttribute("title")??"").toLowerCase(),n=l.getAttribute("data-biotype")??"",a=(""===t||s.indexOf(t)>=0||o.indexOf(t)>=0)&&(null===e||n===e);l.style.display=a?"":"none"}let l=(i??this.element).querySelectorAll(".hw-triplet-chip");for(let i=0;i<l.length;i++){let r=l[i],s=[r.getAttribute("data-triplet")??"",r.getAttribute("data-sugar")??"",r.getAttribute("data-base")??"",r.getAttribute("data-linker")??""].join(" ").toLowerCase(),o=(""===t||s.indexOf(t)>=0)&&null===e;r.style.display=o?"":"none"}let s=(i??this.element).querySelectorAll(".hw-palette__group");for(let t=0;t<s.length;t++){let e=s[t],i=e.querySelectorAll(".hw-palette__tile, .hw-triplet-chip"),r=!1;for(let t=0;t<i.length;t++)if("none"!==i[t].style.display){r=!0;break}r?(e.removeAttribute("hidden"),e.removeAttribute("data-section-empty")):(e.setAttribute("hidden",""),e.setAttribute("data-section-empty","true"))}}_updatePrimedClasses(){let t=this._editor.getNextAddSymbol(),e=this.element.querySelectorAll(".hw-palette__tile");for(let i=0;i<e.length;i++){let r=e[i],l=r.getAttribute("data-symbol")??"",s=r.getAttribute("data-biotype")??"",o=null!==t&&t.symbol===l&&t.biotype===s,n=(r.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-palette__tile--primed"!==t).join(" ");r.setAttribute("class",o?`${n} hw-palette__tile--primed`:n),r.setAttribute("aria-pressed",o?"true":"false")}}_applyActiveTabClasses(){let t=this.element.querySelectorAll(".hw-palette__tab");for(let e=0;e<t.length;e++){let i=t[e],r=i.getAttribute("data-tab")??"";i.setAttribute("aria-selected",r===this._activeTab?"true":"false")}let e=this.element.querySelectorAll(".hw-palette__pane");for(let t=0;t<e.length;t++){let i=e[t];(i.getAttribute("data-tab")??"")===this._activeTab?i.removeAttribute("hidden"):i.setAttribute("hidden","")}}_localStorage(){if(!this._opts.allowFavorites)return null;let t=this._doc.defaultView;if(null==t)return null;try{return t.localStorage??null}catch{return null}}_resolveInitialTab(t){if(void 0!==t&&xt.includes(t))return t;let e=this._localStorage();if(null!==e)try{let t=e.getItem(Lt);if(null!==t&&xt.includes(t))return t}catch{}return Nt}_persistActiveTab(){let t=this._localStorage();if(null!==t)try{t.setItem(Lt,this._activeTab)}catch{}}_loadFavorites(){let t=this._localStorage();if(null!==t){try{let e=t.getItem(Bt);if(null!==e&&""!==e){let t=JSON.parse(e),i=this._extractSymbols(t);for(let t of i)this._favorites.add(t);for(let e of this._extractTriplets(t))this._favoriteTriplets.push(e);return}}catch{}try{let e=t.getItem("hwe.palette.favorites");if(null===e||""===e)return;let i=JSON.parse(e);if(Array.isArray(i)){for(let t of i){if("string"!=typeof t)continue;let e=t.indexOf("|"),i=e>=0?t.slice(e+1):t;""!==i&&this._favorites.add(i)}this._saveFavorites()}}catch{}}}_extractSymbols(t){if(Array.isArray(t)){let e=[];for(let i of t)"string"==typeof i&&e.push(i);return e}if(null!==t&&"object"==typeof t){let e=t;if(Array.isArray(e.symbols)){let t=[];for(let i of e.symbols)"string"==typeof i&&t.push(i);return t}}return[]}_extractTriplets(t){if(null===t||"object"!=typeof t)return[];let e=t;if(!Array.isArray(e.triplets))return[];let i=[];for(let t of e.triplets){if(null===t||"object"!=typeof t)continue;let e=t;"string"==typeof e.sugar&&"string"==typeof e.base&&"string"==typeof e.linker&&i.push({sugar:e.sugar,base:e.base,linker:e.linker})}return i}_saveFavorites(){let t=this._localStorage();if(null!==t)try{let e={symbols:Array.from(this._favorites)};this._favoriteTriplets.length>0&&(e.triplets=this._favoriteTriplets.map(t=>({...t}))),t.setItem(Bt,JSON.stringify(e))}catch{}}};Pt._DEFAULT_TRIPLET_BASES=["A","C","G","U","T"],Pt._PALETTE_RDKIT_CACHE_LIMIT=256;new Set([d.PEPTIDE,d.RNA,d.CHEM,d.BLOB]),new Set(["Backbone","Branch","Terminal","Undefined"]);var $t,Ft;!function(t){t[t.default=0]="default",t[t.continuous=1]="continuous"}($t||($t={})),function(t){t.Sequence="sequence",t.Helm="notation",t.Properties="properties",t.StructureView="structureview"}(Ft||(Ft={}));const Rt={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M  RGP",V2K_A_LINE:"A  ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:"  0  0  0  0  0  0            999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M  V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M  V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M  V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M  V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M  V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M  V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M  V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M  V30 ",V3K_END:"M  END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:d.RNA,symbol:"d"},RIBOSE:{polymerType:d.RNA,symbol:"r"},PHOSPHATE:{polymerType:d.RNA,symbol:"p"},OXYGEN:"O",HYDROGEN:"H"};function Ot(t,e){return t[e.polymerType]?.[e.symbol]}var Dt;!function(t){t[t.SUGAR=0]="SUGAR",t[t.BASE=1]="BASE",t[t.PHOSPHATE=2]="PHOSPHATE",t[t.TERMINAL_5P=3]="TERMINAL_5P",t[t.TERMINAL_3P=4]="TERMINAL_3P"}(Dt||(Dt={}));class Ht extends Map{constructor(t){super(t)}}class Vt{constructor(t,e){this.molfile=t,this.monomers=e}static createEmpty(){return new Vt("",new Ht(null))}}const Gt=d;var Kt,zt,Ut;new RegExp("[rd]\\((\\w)\\)p?","g");class qt{constructor(t,e,i){this.name=t,this.alphabet=e,this.cutoff=i}}!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(Kt||(Kt={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(zt||(zt={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions",t.positionShift=".positionShift",t.selectedPosition=".selectedPosition",t.polymerTypeColumnName=".polymerTypeColumnName",t.annotations=".annotations",t.numberingScheme=".numberingScheme",t.annotationColumnName=".annotationColumnName"}(Ut||(Ut={}));const jt=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};function Wt(t){let e;switch(t){case s:case l:case o:case h:case"nucleotide":e=d.RNA;break;case r:e=d.PEPTIDE;break;case n:e=d.CHEM;break;case a:e=d.BLOB;break;default:e=d.PEPTIDE,console.warn(`Unexpected HelmType '${t}'`)}return e}function Yt(t,e,i,r,l){if(0===t.length)return Vt.createEmpty();const s=r===Gt.RNA&&!!l&&l.length===t.length,{atomCount:o,bondCount:n,needsCapping:a}=function(t,e,i,r,l,s){let o=0,n=0,a=0,h=!0,d=null,u=null;for(let i=0;i<t.length;++i){const r=t[i];if(""!==r.symbol){if("*"==r.symbol)throw new Error("Gap canonical symbol is '', not '*");d=Ot(e,{symbol:r.symbol,polymerType:Wt(r.biotype)}),o+=d.atoms.x.length,n+=d.bonds.bondTypes.length,a++,l&&i%3==2&&(u=d)}}if(r===Gt.PEPTIDE)o+=1,n+=a,a>0&&((d?.meta?.rNodes?.length??0)<2||d?.terminalR2Atom?.toLowerCase()===Rt.HYDROGEN.toLowerCase())&&(h=!1,o-=1,n-=1);else if(l)n+=a,s&&s.length>0&&s[s.length-1]===Dt.TERMINAL_3P?(h=!1,n-=1):o+=1;else{const r=i===zt.DNA?Ot(e,Rt.DEOXYRIBOSE):Ot(e,Rt.RIBOSE),l=Ot(e,Rt.PHOSPHATE);o+=(t.length-1)*l.atoms.x.length,o+=t.length*r.atoms.x.length,o+=1,n+=(t.length-1)*l.bonds.bondTypes.length,n+=t.length*r.bonds.bondTypes.length,n-=1,n+=3*t.length}return{atomCount:o,bondCount:n,needsCapping:h}}(t,e,i,r,s,l),h=new Array(o),d=new Array(n);let u,c=null,p=null;r===Gt.PEPTIDE?u=Xt:(u=Jt,s||(c=i===zt.DNA?Ot(e,Rt.DEOXYRIBOSE):Ot(e,Rt.RIBOSE),p=Ot(e,Rt.PHOSPHATE)));const _={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},b={sugar:c,phosphate:p,seqLength:s?Math.ceil(t.length/3):t.length,atomCount:o,bondCount:n},f=new Ht,m=[];let g,v=0;if(s)!function(t,e,i,r,l,s,o,n,a,h){for(let o=0;o<t.length;++o){const d=t[o];if(""===d.symbol)continue;const u=e[o],c=Ot(i,{symbol:d.symbol,polymerType:Wt(d.biotype)}),p=s.nodeShift,_=s.bondShift;s.i=o,u===Dt.BASE?Qt(c,r,l,s):Zt(c,r,l,s),c.stereoAtoms?.forEach(t=>a.push(t+v)),h(c.atoms.x.length);const b=[];for(let t=p;t<s.nodeShift;++t)b.push(t);const f=[];for(let t=_;t<s.bondShift;++t)f.push(t);n.set(o,{biotype:d.biotype,symbol:d.symbol,atoms:b,bonds:f})}}(t,l,e,h,d,_,0,f,m,t=>{v+=t});else for(_.i=0;_.i<b.seqLength;++_.i){const i=t[_.i];if(""===i.symbol)continue;const r=Ot(e,{symbol:i.symbol,polymerType:Wt(i.biotype)});g=r.terminalR2Atom;const l=_.nodeShift,s=_.bondShift;u(r,h,d,_,b),r.stereoAtoms?.forEach(t=>m.push(t+v)),v+=r.atoms.x.length;const o=_.nodeShift-l,n=new Array(o);for(let t=0;t<o;++t)n[t]=l+t;const a=_.bondShift-s,c=new Array(a);for(let t=0;t<a;++t)c[t]=s+t;f.set(_.i,{biotype:i.biotype,symbol:i.symbol,atoms:n,bonds:c})}a&&function(t,e,i,r,l=Rt.OXYGEN){const s=i.nodeShift+1;t[r.atomCount]=Rt.V3K_BEGIN_DATA_LINE+s+" "+(l??Rt.OXYGEN)+" "+ee(i.backbonePositionShift[0])+" "+i.flipFactor*ee(i.backbonePositionShift[1])+" 0.000000 0\n";const o=i.backboneAttachNode,n=s;e[r.bondCount]=Rt.V3K_BEGIN_DATA_LINE+i.bondShift+" 1 "+o+" "+n+"\n"}(h,d,_,b,g??Rt.OXYGEN);const y=Rt.V3K_BEGIN_COUNTS_LINE+o+" "+n+Rt.V3K_COUNTS_LINE_ENDING;let w="";return w+=Rt.V3K_HEADER_FIRST_LINE,w+=Rt.V3K_HEADER_SECOND_LINE,w+=Rt.V3K_BEGIN_CTAB_BLOCK,w+=y,w+=Rt.V3K_BEGIN_ATOM_BLOCK,w+=h.join(""),w+=Rt.V3K_END_ATOM_BLOCK,w+=Rt.V3K_BEGIN_BOND_BLOCK,w+=d.join(""),w+=Rt.V3K_END_BOND_BLOCK,m.length>0&&(w+=function(t){const e=[];let i=`M  V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let r=0;r<t.length;r++){const l=`${i} ${t[r]}`;l.length>76?(e.push(`${i} -\n`),i=`M  V30 ${t[r]}`):i=l,r===t.length-1&&e.push(`${i})\n`)}return`M  V30 BEGIN COLLECTION\n${e.join("")}M  V30 END COLLECTION\n`}(m)),w+=Rt.V3K_END_CTAB_BLOCK,w+=Rt.V3K_END,{molfile:w,monomers:f}}function Xt(t,e,i,r){r.flipFactor=(-1)**(r.i%2),Zt(t,e,i,r)}function Zt(t,e,i,r){!function(t,e,i){for(let r=0;r<t.atoms.atomTypes.length;++r){const l=i.nodeShift+r+1;e[i.nodeShift+r]=Rt.V3K_BEGIN_DATA_LINE+l+" "+t.atoms.atomTypes[r]+" "+ee(i.backbonePositionShift[0]+t.atoms.x[r])+" "+ee(i.backbonePositionShift[1]+i.flipFactor*t.atoms.y[r])+" "+t.atoms.kwargs[r]}}(t,e,r),te(t,i,r),function(t,e,i){if(0!==i.backboneAttachNode){const r=i.bondShift,l=i.backboneAttachNode,s=t.meta.terminalNodes[0]+i.nodeShift;e[i.bondShift-1]=Rt.V3K_BEGIN_DATA_LINE+r+" 1 "+l+" "+s+"\n"}}(t,i,r),null!==t.meta.branchShift&&t.meta.terminalNodes.length>2&&function(t,e){e.branchAttachNode=e.nodeShift+t.meta.terminalNodes[2];for(let i=0;i<2;++i)e.branchPositionShift[i]=e.backbonePositionShift[i]+t.meta.branchShift[i]}(t,r),function(t,e){e.backboneAttachNode=e.nodeShift+t.meta.terminalNodes[1],e.bondShift+=t.bonds.atomPairs.length+1,e.nodeShift+=t.atoms.atomTypes.length,e.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,e.backbonePositionShift[1]+=e.flipFactor*(t.meta.backboneShift?.[1]??0)}(t,r)}function Jt(t,e,i,r,l){if(0===r.i)Zt(l.sugar,e,i,r);else for(const t of[l.phosphate,l.sugar])Zt(t,e,i,r);Qt(t,e,i,r)}function Qt(t,e,i,r){!function(t,e,i){for(let r=0;r<t.atoms.atomTypes.length;++r){const l=i.nodeShift+r+1;e[i.nodeShift+r]=Rt.V3K_BEGIN_DATA_LINE+l+" "+t.atoms.atomTypes[r]+" "+ee(i.branchPositionShift[0]+t.atoms.x[r])+" "+ee(i.branchPositionShift[1]+i.flipFactor*t.atoms.y[r])+" "+t.atoms.kwargs[r]}}(t,e,r),te(t,i,r),function(t,e,i){const r=i.bondShift,l=i.branchAttachNode,s=t.meta.terminalNodes[0]+i.nodeShift;e[r-1]=Rt.V3K_BEGIN_DATA_LINE+r+" 1 "+l+" "+s+"\n"}(t,i,r);const l=r.bondShift,s=r.branchAttachNode,o=t.meta.terminalNodes[0]+r.nodeShift;i[l-1]=Rt.V3K_BEGIN_DATA_LINE+l+" 1 "+s+" "+o+"\n",r.bondShift+=t.bonds.atomPairs.length+1,r.nodeShift+=t.atoms.atomTypes.length}function te(t,e,i){for(let r=0;r<t.bonds.atomPairs.length;++r){const l=i.bondShift+r+1,s=t.bonds.atomPairs[r][0]+i.nodeShift,o=t.bonds.atomPairs[r][1]+i.nodeShift;let n="";if(t.bonds.bondConfiguration.has(r)){let e=t.bonds.bondConfiguration.get(r);i.flipFactor<0&&(e=1===e?3:1),n=" CFG="+e}const a=t.bonds.kwargs.has(r)?" "+t.bonds.kwargs.get(r):"";e[i.bondShift+r]=Rt.V3K_BEGIN_DATA_LINE+l+" "+t.bonds.bondTypes[r]+" "+s+" "+o+n+a+"\n"}}function ee(t){return Math.round(Rt.PRECISION_FACTOR*t)/Rt.PRECISION_FACTOR}new qt(zt.PT,jt.fasta.peptide,.5),new qt(zt.DNA,jt.fasta.dna,.55),new qt(zt.RNA,jt.fasta.rna,.55),Kt.FASTA,Kt.SEPARATOR,Kt.HELM,Kt.BILN,onmessage=t=>{const{seqList:e,rolesList:i,monomersDict:r,alphabet:l,polymerType:s,start:o,end:n}=t.data,a=new Array(n-o),h=new Array(0);for(let t=o;t<n;++t)try{const n=e[t],h=i?i[t]:void 0;a[t-o]=Yt(n,r,l,s,h)}catch(e){const i=`Cannot get molfile of row #${t}: ${e instanceof Error?e.message:e.toString()}.`;h.push(i)}postMessage({molfiles:a,warnings:h})},helm={}})();
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